Pages

Thursday, 26 November 2015

My review of DNA Cymru Part 2 - the controversy continues

I wrote earlier on this year about the controversy over the DNA Cymru series on the Welsh-language TV channel S4C. The first programme in the series was broadcast on St David's Day. A further four programmes were planned and the first of these was shown on Sunday. The programme can be seen on the BBC iPlayer with English subtitles, and is available online for the next 28 days. There is also a DNA Cymru website to accompany the new series.

The criticisms clearly touched a raw nerve because in Sunday's programme some time was spent trying to address the concerns. However, the programme makers appear to have misunderstood the nature of the complaints, and they failed to tackle some of the biggest issues. The programme was also very one-sided and they did not give any of their critics the opportunity to voice their criticisms in person. Nevertheless it was a big improvement on the first programme, the claims were not quite so extravagant, and they did include some real science that was mixed in with the storytelling, although it is notable that the real science was coming from independent and credible scientists like Professor Dan Bradley and Professor Peter Donnelly, and not from the ‘tests’ performed by CymruDNAWales

Phylogeography
The programme tried somewhat unnecessarily to defend the concept of phylogeography yet, as far as I'm aware, no scientist is critical of this concept. Phylogeography is the process of matching a genealogical lineage with its present-day geographical distribution. In human evolutionary studies the process is often applied to the phylogenetic trees of mitochondrial DNA and Y-chromosome DNA. The mtDNA tree is published on the Phylotree website. ISOGG (the International Society of Genetic Genealogy) maintains the Y-DNA tree. There is also a minimal reference version of the Y-tree on the Phylotree website. The different branches of the Y-DNA and mtDNA trees refer to different haplogroups, and these haplogroups can be divided into subhaplogroups and ultimately haplotypes. The different branches of the Y-DNA and mtDNA tree often have distinct geographical distribution patterns. This information can in itself sometimes be informative for genealogical purposes and also for forensics.

While phylogeography in itself is a perfectly valid term to describe the present-day geographical distribution of known lineages, issues arise when it comes to making inferences about the geographical origins of those lineages in the past and of the population history that shaped the phylogeography. The most common approach to this is known as interpretative phylogeography. It is the interpretative aspect that is questioned by the majority of population geneticists (Balloux 2009, Chikhi 2010, Goldstein and Chikhi 2002). Interpretative approaches are, by definition, highly subjective, and can easily be influenced by the preconceived biases or research agendas of the researchers.

By testing the Y-DNA and mtDNA of living people we can learn about the present-day distribution of the different haplogroups, but it is much more difficult to make inferences about the past from modern DNA. Our ancestry is convoluted and very complicated, and is confounded by migration, genetic drift and population size changes in the past. Throughout human history migration has been the rule rather than the exception, and we now know from empirical data that "the current inhabitants of a region are often poor representatives of the populations that lived there in the distant past" (Pickrell and Reich 2014). There is also considerable uncertainty in the dating of the different branches of the Y-DNA and mtDNA trees. Nevertheless, despite these limitations there are some researchers who still try to link Y-DNA and mtDNA haplogroups with specific tribes and historical events. It is, of course, very easy to make such associations and – given the flexibility of interpretative phylogeography – to make the data fit your favourite hypothesis, but there are almost always many different explanations that would fit the available data (Nielsen and Beaumont 2009).

In addition, Y-DNA and mtDNA represent an increasingly smaller percentage of our ancestry as we go further back in time, and consequently they are only weakly informative about our deep ancestry. Y-DNA and mtDNA are also more prone to the problems of genetic drift. However, despite the limitations for deep ancestry, Y-DNA and mtDNA tests are very useful for genealogical purposes where the results can be analysed in combination with genealogical and historical documents.

Ancient DNA is now beginning to transform our knowledge of the past. Although only a limited number of Y-DNA and mtDNA samples are available it is already very clear that the distribution and frequency of Y-DNA and mtDNA haplogroups were very different in the past. With the new next generation sequencing methodologies it is possible to sequence the entire genome whereas early ancient DNA studies focused mainly on mitochondrial DNA.

Real science
The DNA Cymru programme did feature some real science. There were interviews with Professor Sir Walter Bodmer and Professor Peter Donnelly from the People of the British Isles Project (POBI). This project is based at the University of Oxford. They published a landmark paper on the genetic composition of the British Isles earlier this year (Leslie et al 2015). The POBI paper was based on analysis of autosomal DNA, but Y-DNA and mtDNA have also been extracted, and Professor Mark Jobling at the University of Leicester is in the process of analysing these results. This should provide a useful insight into the geographical distributions of the Y-DNA and mtDNA haplogroups of the British Isles. It is strange that the programme makers do not seem to have been aware of this Y-DNA and mtDNA research prior to arranging their partnership with a commercial company to do the same type of testing.

Professor Dan Bradley of Trinity College Dublin was interviewed about his ancient DNA research. He is sequencing 30 DNA samples "across the whole pre-history of Ireland". He says "It's almost like dropping a plumb line through history". He cautioned about making inferences from modern DNA: "There's one problem about looking at the present to study the past, and that is, essentially, the past is a different country. The models we bring up from the present to understand the past may miss big things". He cited the example of Ötzi the Iceman who was found in the Alps but who has a genetic signature which is more like the people of the southern Mediterranean.

The programme also featured interviews with other academics. Archaeologist Rhys Mwyn described Brymbo Man, a Bronze Age skeleton whose burial was typical of the Beaker People. Brymbo Man's DNA has not yet been tested but it would be an interesting study. The linguist and historian John Koch discussed the migration of the Beaker People.

It is not clear how much the academics who agreed to appear on the programme knew about the nature of the collaboration with CymruDNAWales/ScotlandsDNA. The S4C website does state: It’s important to remember that - except where they comment specifically on screen in the programmes – their involvement should not be read as an endorsement of commercial DNA testing". I noticed earlier this week that the text had been changed to clarify that "their involvement should not be read as an endorsement of commercial DNA testing or inferences made from such data", no doubt after concerns were raised by some of the credible scientists interviewed.

Celebrity DNA
The credible science was interspersed with stories about three Welsh celebrities – Caryl Parry Jones, Roy Noble and Ken Owens – who received their DNA results from CymruDNAWales on the programme. Roy Noble was told that his G2a haplogroup was found in the first people who brought farming to Europe. Ken Owens was told that his R1b sub-haplogroup S145 (L21) was brought to Wales with the Beaker People. However, we do not have any way of knowing when these haplogroups appeared in Wales and this is pure speculation. By mixing up the company's storytelling with legitimate scientific research from respected scientists like Dan Bradley and Peter Donnelly, the company are no doubt hoping that some of that credibility rubs off on their own "findings". Unfortunately viewers who are not familiar with the scientific literature might not realise where the legitimate science ends and the storytelling begins.

Commercial interests
The minimum standard for scientific credibility is publication in a peer-reviewed scientific journal. Unfortunately none of the "research" from the CymruDNAWales project has been published anywhere. It is in any case unlikely to get through the peer review process in a respected journal. In order to participate in the DNA Cymru "project" it is necessary to order an expensive DNA test from CymruDNAWales. Consequently the samples are likely to be very biased.

It was reported in the programme on Sunday that DNA Cymru had conducted tests on 1000 people. It seems highly likely that many of these people were encouraged to pay for a test after seeing the launch programme. I note too that the tests are still being surreptitiously promoted on the S4C website. Visitors are invited to click on a link to find out more about the CymruDNAWales "project" but the link provides no information about a scientific research project; instead it takes you to the Moffat Partnership's CymruDNAWales website where you can buy one of their ancestry tests.

We learnt from the programme that the principal scientist for the DNA Cymru series is Dr Jim Wilson. It just so happens that he is also the Chief Scientific Officer of CymruDNAWales and the other associated companies. He is a director of the Moffat Partnership and is a major shareholder with the company. His company, and in particular his business partner Alistair Moffat, have been heavily criticised for manipulating the press and misleading the public with their outrageous stories. At UCL we set up a whole website to counter these unscientific claims, an initiative which has been very well received by the academic community. One is therefore left wondering if the choice to partner with this company was made not as an independent editorial decision but as a result of the friendship of S4C's CEO Ian Jones with Alistair Moffat.

I should clarify that the Chromo 2 test sold by ScotlandsDNA is a perfectly valid test if you are interested in learning about your Y-chromosome and mitochondrial DNA markers. It is only the haplogroup reports provided by the company that have no scientific validity. There is nothing wrong with a TV company using the services of a commercial company. However, S4C, as a public service broadcaster, is bound by strict editorial guidelines to ensure that its impartiality and integrity are not compromised. It has a duty to provide accurate content which is not influenced by commercial interests.

Although the programme was better than the previous one, this is mainly because they incorporated highly respected scientists like Dan Bradley and Peter Donnelly. It is still a big disappointment to see a public service broadcaster being used to promote a commercial genetic ancestry company in the guise of a research project, and to see speculative stories mixed up in such a misleading way with serious science.

Further reading
For more information on the problems of making inferences about deep ancestry from Y-DNA and mitochondrial DNA see the pamphlet Sense About Genetic Ancestry Testing from Sense About Science. This guide was written by my colleagues at UCL Professor Mark Thomas and Professor David Balding in collaboration with some of the big names in population genetics: Dr Turi King, Dr Lounès Chikhi, Dr Rosalind Harding, Professor Mark Jobling and Professor Guido Barbujani.

11 comments:

The issue remains that no Y-STR testing is going to be discussed in these programmes, so all of this predates any application to conventional family history timelines. And L21+ is certainly not specific for Wales. I test +ve for L21 and my historical family comes from Norfolk.

Bradley's research will be very interesting when it's published as a Paper. The folks in TCD (Trinity College Dublin) and UCD (Univeristy College Dublin) are heavily involved in recent papers using the Petrous bone to retrive viable aDNA (for example the first African aDNA genome recovered etc.)

If they have 30 full genomes from Ireland' prehistory it will provide a major benchmark to compare modern Northwest European populations against. At the moment there's no aDNA from Ireland published, I believe there's a total of 10 samples from Britain (3 x Iron age, 7 x Anglo-Saxon era).

It wouldn't surprise me if we have up to 500 Western Eurasian aDNA genomes within the next 18 months. I do hope Bradley's research will spur Irish archaelogists into further collaboration, there's number of large Iron age/Early Christian cemetries that were found in last 10 years in Ireland due to "Celtic Tiger" era construction/road building etc.

As for claims about L21 and Beaker, it would be nice to actually have a beaker remain that was verified L21+ first ;)

Though of course the genome from Southern Germany was at least in "brother clade" of U152 (P312+/U152+ vs. P312+/L21+)

This is fascinating. I say that in a slightly 'What he hell is she talking about way' because my knowledge of DNA is on a par with my fluency in Old Prussian. Even so, I stuck with it, and I now know a lot more than I did before.

Though my interest in this S4C project is due entirely to having read Moffatt's books on the 'history' his native Kelso; my fascination with what might lie beneath the unexcavated mound mentioned in that blog post of mine you link to; my nose for an individual, group or project that's a bit iffy; and the fact that, being Welsh, I am overwhelmed with such material for my blog.

If it's OK with you I shall link the article on my blog to this post. I'm sure it will make sense to my erudite readers.

Paul, I think we can expect an explosion of ancient DNA material in the next few years. We still have nothing from Ireland, Scotland or Wales. The Hinxton genomes and Richard III are the only ones from England. I would expect the Beaker people to have multiple haplogroups just as we see today with any cultural group. There will never be enough ancient DNA samples for us to know the full distribution pattern of any haplogroup in the past, but it will still be interesting to have some results from contemporaneous remains to give us some of the picture. I predict there will be some surprises in store for everyone.

Jac, Do feel free to share my blog post with your readers. I had to go into some of the technical details to try and rebut some of the misleading claims on the programme. Essentially they misusing a technique that applies to the present to apply it to the past. They are trying to make out that their critics are the exception rather than the rule. In reality there is hardly anyone who supports the approach of "interpretative phylogeography". They did get the support of one scientist on the programme, but he's one of only a few people left who still work this way, apart from the company that are doing the testing for the programme!

There are also concerns about what Moffat is doing in Scotland. See the entry for 23rd October on our timeline:

Not sure if Richard III genome has been published but there are actually 10 aDNA genomes from Britain currently available, 2 are from Hinxton (Iron age), there's another Iron age one and than the 7 female genomes from Anglo-Saxon period. These were detailed in the recent paper.

http://biorxiv.org/content/early/2015/07/17/022723

It's gonna get interesting when we start to see Mesolithic, Neolithic and Bronze age genomes. Of course one thing we can say about ancient samples and Y-DNA is they do provide baselines for minimum age of specific haplogroups. So for example at least with German Bell Beaker, we know that U152 is as least that old (ergo P312 has to be older).

The Richard III genome hasn't yet been published. I imagine it's probably going to be another year or so before that paper appears. I knew the Hinxton stuff was in BioRxiv but I don't think it's actually been published in a journal as yet. The Museum of London have also started to do some DNA testing on their skeleton collection. Ancient DNA will certainly be very helpful for dating purposes.

DK said: "... Y-DNA and mtDNA have also been extracted, and Professor Mark Jobling at the University of Leicester is in the process of analysing these results." This should provide a useful insight into the geographical distributions of the Y-DNA and mtDNA haplogroups of the British Isles. It is strange that the programme makers do not seem to have been aware of this Y-DNA and mtDNA research prior to arranging their partnership with a commercial company to do the same type of testing."

The PoBI Chip Y-DNA "fixed based" SNPs are circa 2010 ... 5 years old. The PoBI tests does not include more advanced "discovery" testing for Y-DNA SNPs such as is done by FTDNA BIGY and the far better FGC tests. There have been a vast amount of new Y-DNA SNPs discovered in the past 5 years which the outdated "fixed based SNP Chip" will never show anything for. As an example, the ~43 Ancient British R1b-L371 Y-DNA SNPs will never show up on the PoBI paper Jobling is doing (he told me as much)

So DK, I question your expertise and narrative when you state: "... should provide a useful insight into the geographical distributions of the Y-DNA haplogroups".

Such insights you mention that Jobling will report concerning the finer scale terminal haplogroups just ain't going to happen. I hope you will issue a clarification and correction on this.

You and Mark Thomas are obviously biased in this area and you are the one who needs some Sense about Science.

George, The advantage of the POBI dataset is that is unbiased. Obviously you won't get the fine detail with chip testing but it will give a better idea of the distribution than using FTDNA's skewed dataset with a big US bias.

You must be joking when you conflate and confuse the purposes for FTDNA and PoBI. Such confusion on your part demonstrates your need for a greater dose of "Sense about Science"

FTDNA is consumer based and open to all comers whereas PoBI is academic based and screened out 95% plus of the British population. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260910/

FTDNA is aimed at lay and non-academic Genetic Genealogists whereas PoBI is aimed at academic Population Geneticists.

FTDNA is used by non-academic persons seeking to learn more about their family ancestors in the past 600 or so years whereas PoBI is used by academics seeking to learn more about broader population groups and their distribution and movements in the past 6,000 or so years.

However, many who use FTDNA have advanced several steps and joined together in groups such as the 'Wales Discovery Group'. We have our DNA tested at FTDNA BIGY/ FGC Elite, YSEQ, and yes even at Jim Wilson's company. We know what we are doing and I can assure you that our R1b-L371 Hg ancestry is 'Ancient British'

I was talking purely about Y-DNA whereas the principal area of PoBI was the use of Autosomal DNA .... Y-DNA and Mt-DNA were an afterthought. In Genetic Genealogy "we do" look at surnames and "we do" look at geographic places where a person was born and died as well as other geographic indicators such as a the passenger records from where/when a ship sailed to and from.

I can assure you that Jobling's paper will never have a discussion on surnames/Hgs&STRs nor surnames/fine geographic distribution nor Hgs&STRs/fine geographic distributions. The Wellcome Trust confidentiality / anonymity preamble of this study would never approve such and you should know that. http://www.nature.com/news/privacy-protections-the-genome-hacker-1.12940#/ref-link-1

So speaking of US biases, I am darn glad that in 1620 some pioneering Pilgrims left your "Old World" to my "New World". Has your honorary UCL degree led to a "Sense about History" that a 'Jones' was the Ship Master on the Mayflower? Do you know his YDNA Hg?

Debbie, I am tiring of your demeaning attitude about the US and US based Genetic Genealogists. And, I am also tiring of your attacks on Jim Wilson and his company ... is this inspired by your friend Mark Thomas and others at UCL?

George, I am perfectly aware of the differences between FTDNA and POBI and I know how genetic genealogy works. I am not being demeaning to US and US based genetic genealogists. If you want a representative sample for a surname project you need to ensure that you test people from all over the world, and not just one country. There are some lines that will only be found in the US and others that will only be found in the UK or Australia. Genetic drift can be a big problem sometimes with emigrant lines.

Please can you refrain from posting personal attacks on my blog and from posting the contents of e-mails that were sent to you privately. I've deleted one of your comments for this reason.

About Me

Subscribe via email

Subscribe Now

My books

Copyright

The material on these pages is copyright Debbie Kennett or reproduced with permission from other copyright owners. It may be downloaded and printed for personal reference, but not otherwise copied, altered in any way or transmitted to others (unless explicitly stated otherwise) without the written permission of Debbie Kennett.

StatCounter

Followers

Copyright

The material on these pages is copyright Debbie Kennett or reproduced with permission from other copyright owners. It may be downloaded and printed for personal reference, but not otherwise copied, altered in any way or transmitted to others (unless explicitly stated otherwise) without the written permission of Debbie Kennett.